Re: [Rdkit-devel] Beta of Q1 2016 release now up

[Greg L. <gre...@gm...>]

Hi Gianluca,

On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna <gi...@gm...> wrote:

>
> But no joy still....
>
>
> [ 36%] Building CXX object
> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o
> cd
> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse
> && /usr/bin/c++   -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHR
> EADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS
> -I/usr/include/python2.7
> -I/builddir/build/BUILD/rdkit-Release_2016_03_1b1/pyt
> hon2/Code  -O2 -g -pipe -Wall -Werror=format-security
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong
> --param=ssp-buffer-size=
> 4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
> -m64 -mtune=generic  -mpopcnt -Wno-deprecated -Wno-unused-function -f
> no-strict-aliasing -fPIC -Wall -Wextra -O2 -g -DNDEBUG -fPIC
> -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o
> CMakeFiles/SmilesParse.dir/lex.yys
> marts.cpp.o -c
> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmarts.cpp
> smiles.ll:40:52: error: 'yyscan_t' has not been declared
>  size_t setup_smiles_string(const std::string &text,yyscan_t yyscanner){
>                                                     ^
> smiles.ll: In function 'size_t setup_smiles_string(const string&, int)':
> smiles.ll:49:46: error: too many arguments to function 'void*
> yysmiles_alloc(yy_size_t)'
>    buf = (char *) yysmiles_alloc(n ,yyscanner );
>                                               ^
>
> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:326:7:
> note: declared here
>  void *yysmiles_alloc (yy_size_t  );
>        ^
> smiles.ll:69:45: error: too many arguments to function
> 'yy_buffer_state* yysmiles__scan_buffer(char*, yy_size_t)'
>    b = yysmiles__scan_buffer(buf,n ,yyscanner);
>                                              ^
>
> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:322:17:
> note: declared here
>  YY_BUFFER_STATE yysmiles__scan_buffer (char *base,yy_size_t size  );



Something odd is going on with the output of flex. The easiest way to "fix"
this is just to avoid the problem by not running flex/bison yourself.

If that would be ok, you can just change the cmake command line argment
-D RDK_USE_FLEXBISON:BOOL=ON
to
-D RDK_USE_FLEXBISON:BOOL=OFF

-greg